+Open data
-Basic information
Entry | Database: PDB / ID: 4j4l | ||||||
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Title | Modular evolution and design of the protein binding interface | ||||||
Components |
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Keywords | PROTEIN BINDING/CYTOKINE / LRR / IL-6 binding / Interleukin 6 / extracellular matrix / PROTEIN BINDING-CYTOKINE complex | ||||||
Function / homology | Function and homology information positive regulation of interleukin-21 production / regulation of astrocyte activation / glucagon secretion / regulation of glucagon secretion / negative regulation of interleukin-1-mediated signaling pathway / hepatic immune response / regulation of vascular endothelial growth factor production / negative regulation of primary miRNA processing / T follicular helper cell differentiation / germinal center B cell differentiation ...positive regulation of interleukin-21 production / regulation of astrocyte activation / glucagon secretion / regulation of glucagon secretion / negative regulation of interleukin-1-mediated signaling pathway / hepatic immune response / regulation of vascular endothelial growth factor production / negative regulation of primary miRNA processing / T follicular helper cell differentiation / germinal center B cell differentiation / regulation of microglial cell activation / interleukin-6 receptor complex / positive regulation of extracellular matrix disassembly / positive regulation of type B pancreatic cell apoptotic process / positive regulation of receptor signaling pathway via STAT / positive regulation of apoptotic DNA fragmentation / response to peptidoglycan / hepatocyte proliferation / neutrophil apoptotic process / interleukin-6 receptor binding / negative regulation of collagen biosynthetic process / inflammatory response to wounding / T-helper 17 cell lineage commitment / positive regulation of T-helper 2 cell cytokine production / positive regulation of B cell activation / endocrine pancreas development / positive regulation of acute inflammatory response / regulation of neuroinflammatory response / vascular endothelial growth factor production / negative regulation of chemokine production / positive regulation of neuroinflammatory response / positive regulation of platelet aggregation / neutrophil mediated immunity / positive regulation of cytokine production involved in inflammatory response / negative regulation of bone resorption / positive regulation of leukocyte chemotaxis / positive regulation of leukocyte adhesion to vascular endothelial cell / CD163 mediating an anti-inflammatory response / negative regulation of fat cell differentiation / positive regulation of immunoglobulin production / maintenance of blood-brain barrier / interleukin-6-mediated signaling pathway / Interleukin-6 signaling / positive regulation of interleukin-17 production / MAPK3 (ERK1) activation / Interleukin-10 signaling / MAPK1 (ERK2) activation / monocyte chemotaxis / regulation of insulin secretion / positive regulation of interleukin-10 production / humoral immune response / negative regulation of lipid storage / regulation of presynapse assembly / Transcriptional Regulation by VENTX / positive regulation of vascular endothelial growth factor production / positive regulation of osteoblast differentiation / regulation of angiogenesis / positive regulation of epithelial to mesenchymal transition / positive regulation of T cell proliferation / positive regulation of chemokine production / response to glucocorticoid / positive regulation of glial cell proliferation / positive regulation of tyrosine phosphorylation of STAT protein / axonogenesis / response to activity / positive regulation of interleukin-1 beta production / cytokine activity / positive regulation of translation / positive regulation of interleukin-8 production / liver regeneration / acute-phase response / Post-translational protein phosphorylation / positive regulation of smooth muscle cell proliferation / positive regulation of receptor signaling pathway via JAK-STAT / growth factor activity / platelet activation / cellular response to hydrogen peroxide / cellular response to virus / positive regulation of DNA-binding transcription factor activity / negative regulation of neurogenesis / cytokine-mediated signaling pathway / ADORA2B mediated anti-inflammatory cytokines production / neuron cellular homeostasis / positive regulation of interleukin-6 production / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / neuron projection development / positive regulation of tumor necrosis factor production / positive regulation of peptidyl-tyrosine phosphorylation / glucose homeostasis / positive regulation of peptidyl-serine phosphorylation / Senescence-Associated Secretory Phenotype (SASP) / Interleukin-4 and Interleukin-13 signaling / defense response to virus / cellular response to lipopolysaccharide / defense response to Gram-negative bacterium / positive regulation of MAPK cascade / defense response to Gram-positive bacterium / inflammatory response / positive regulation of apoptotic process / negative regulation of cell population proliferation Similarity search - Function | ||||||
Biological species | Listeria monocytogenes (bacteria) synthetic construct (others) Eptatretus burgeri (inshore hagfish) Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | ||||||
Authors | Cheong, H.K. / Kim, H.J. | ||||||
Citation | Journal: To be Published Title: Modular evolution and design of the protein binding interface Authors: Lee, J. / Kim, H.J. / Yang, C. / Choi, J. / Kyeong, H. / Yuk, J. / Park, K. / Kim, Y.J. / Heu, W. / Lee, S. / Kim, D. / Jo, E.K. / Cheong, H.K. / Kim, H.S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4j4l.cif.gz | 176 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4j4l.ent.gz | 138.8 KB | Display | PDB format |
PDBx/mmJSON format | 4j4l.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/j4/4j4l ftp://data.pdbj.org/pub/pdb/validation_reports/j4/4j4l | HTTPS FTP |
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-Related structure data
Related structure data | 1aluS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 30059.117 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 43-100,UNP RESIDUES 141-232 Source method: isolated from a genetically manipulated source Details: CHIMERA OF RESIDUES 43-100 FROM INTERNALIN B, REPEAT MODULES, RESIDUES 141-232 FROM VARIABLE LYMPHOCYTE RECEPTOR B, AND 8 HIS TAGS Source: (gene. exp.) Listeria monocytogenes (bacteria), (gene. exp.) synthetic construct (others), (gene. exp.) Eptatretus burgeri (inshore hagfish) Gene: VLRB / Production host: Escherichia coli (E. coli) / References: UniProt: A4L9V2, UniProt: Q4G1L3 #2: Protein | Mass: 19196.943 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: IL6, IFNB2 / Production host: Escherichia coli (E. coli) / References: UniProt: P05231 #3: Water | ChemComp-HOH / | Sequence details | THE RESIDUE 101-209 REPRESENTS CONSENSUS DESIGNED REPEAT MODULES. THE SEQUENCES OF REPEAT MODULES ...THE RESIDUE 101-209 REPRESENTS | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.34 Å3/Da / Density % sol: 47.49 % |
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Crystal grow | Temperature: 290 K / Method: vapor diffusion / pH: 8 Details: 0.1M magnesium formate, 15-18% w/v polyethylene glycol 3350, pH 8.0, VAPOR DIFFUSION, temperature 290K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-1A / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 5, 2012 |
Radiation | Monochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→61.09 Å / Num. all: 40127 / Num. obs: 38083 / % possible obs: 95.8 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 |
Reflection shell | Resolution: 2.3→2.36 Å / % possible all: 78.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1ALU Resolution: 2.3→61.09 Å / Cor.coef. Fo:Fc: 0.926 / Cor.coef. Fo:Fc free: 0.885 / SU B: 8.243 / SU ML: 0.199 / Cross valid method: THROUGHOUT / ESU R: 0.38 / ESU R Free: 0.269 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 33.539 Å2
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Refinement step | Cycle: LAST / Resolution: 2.3→61.09 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.3→2.36 Å / Total num. of bins used: 20
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